Job ID = 10165783 SRX = SRX9120616 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 28295530 spots for SRR12638559/SRR12638559.sra Written 28295530 spots for SRR12638559/SRR12638559.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166094 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:01 28295530 reads; of these: 28295530 (100.00%) were unpaired; of these: 89597 (0.32%) aligned 0 times 23608487 (83.44%) aligned exactly 1 time 4597446 (16.25%) aligned >1 times 99.68% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4647253 / 28205933 = 0.1648 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:04:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:04:18: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:18: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:04:23: 1000000 INFO @ Thu, 08 Oct 2020 20:04:28: 2000000 INFO @ Thu, 08 Oct 2020 20:04:33: 3000000 INFO @ Thu, 08 Oct 2020 20:04:39: 4000000 INFO @ Thu, 08 Oct 2020 20:04:44: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:04:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:04:47: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:04:47: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:04:49: 6000000 INFO @ Thu, 08 Oct 2020 20:04:53: 1000000 INFO @ Thu, 08 Oct 2020 20:04:55: 7000000 INFO @ Thu, 08 Oct 2020 20:04:58: 2000000 INFO @ Thu, 08 Oct 2020 20:05:01: 8000000 INFO @ Thu, 08 Oct 2020 20:05:04: 3000000 INFO @ Thu, 08 Oct 2020 20:05:06: 9000000 INFO @ Thu, 08 Oct 2020 20:05:10: 4000000 INFO @ Thu, 08 Oct 2020 20:05:12: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:05:15: 5000000 INFO @ Thu, 08 Oct 2020 20:05:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Thu, 08 Oct 2020 20:05:16: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:05:16: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:05:17: 11000000 INFO @ Thu, 08 Oct 2020 20:05:21: 6000000 INFO @ Thu, 08 Oct 2020 20:05:22: 1000000 INFO @ Thu, 08 Oct 2020 20:05:23: 12000000 INFO @ Thu, 08 Oct 2020 20:05:27: 7000000 INFO @ Thu, 08 Oct 2020 20:05:28: 2000000 INFO @ Thu, 08 Oct 2020 20:05:29: 13000000 INFO @ Thu, 08 Oct 2020 20:05:33: 8000000 INFO @ Thu, 08 Oct 2020 20:05:33: 3000000 INFO @ Thu, 08 Oct 2020 20:05:35: 14000000 INFO @ Thu, 08 Oct 2020 20:05:38: 9000000 INFO @ Thu, 08 Oct 2020 20:05:39: 4000000 INFO @ Thu, 08 Oct 2020 20:05:40: 15000000 INFO @ Thu, 08 Oct 2020 20:05:44: 10000000 INFO @ Thu, 08 Oct 2020 20:05:45: 5000000 INFO @ Thu, 08 Oct 2020 20:05:46: 16000000 INFO @ Thu, 08 Oct 2020 20:05:50: 11000000 INFO @ Thu, 08 Oct 2020 20:05:51: 6000000 INFO @ Thu, 08 Oct 2020 20:05:51: 17000000 INFO @ Thu, 08 Oct 2020 20:05:56: 12000000 INFO @ Thu, 08 Oct 2020 20:05:56: 7000000 INFO @ Thu, 08 Oct 2020 20:05:57: 18000000 INFO @ Thu, 08 Oct 2020 20:06:01: 13000000 INFO @ Thu, 08 Oct 2020 20:06:02: 8000000 INFO @ Thu, 08 Oct 2020 20:06:03: 19000000 INFO @ Thu, 08 Oct 2020 20:06:07: 14000000 INFO @ Thu, 08 Oct 2020 20:06:08: 9000000 INFO @ Thu, 08 Oct 2020 20:06:08: 20000000 INFO @ Thu, 08 Oct 2020 20:06:13: 15000000 INFO @ Thu, 08 Oct 2020 20:06:14: 10000000 INFO @ Thu, 08 Oct 2020 20:06:14: 21000000 INFO @ Thu, 08 Oct 2020 20:06:18: 16000000 INFO @ Thu, 08 Oct 2020 20:06:19: 11000000 INFO @ Thu, 08 Oct 2020 20:06:19: 22000000 INFO @ Thu, 08 Oct 2020 20:06:24: 17000000 INFO @ Thu, 08 Oct 2020 20:06:25: 12000000 INFO @ Thu, 08 Oct 2020 20:06:25: 23000000 INFO @ Thu, 08 Oct 2020 20:06:28: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:06:28: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:06:28: #1 total tags in treatment: 23558680 INFO @ Thu, 08 Oct 2020 20:06:28: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:06:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:06:29: #1 tags after filtering in treatment: 23558680 INFO @ Thu, 08 Oct 2020 20:06:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:06:29: #1 finished! INFO @ Thu, 08 Oct 2020 20:06:29: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:06:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:06:29: 18000000 INFO @ Thu, 08 Oct 2020 20:06:30: #2 number of paired peaks: 148 WARNING @ Thu, 08 Oct 2020 20:06:30: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Thu, 08 Oct 2020 20:06:30: start model_add_line... INFO @ Thu, 08 Oct 2020 20:06:30: start X-correlation... INFO @ Thu, 08 Oct 2020 20:06:30: end of X-cor INFO @ Thu, 08 Oct 2020 20:06:30: #2 finished! INFO @ Thu, 08 Oct 2020 20:06:30: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:06:30: #2 alternative fragment length(s) may be 1,24,42,525,540,553 bps INFO @ Thu, 08 Oct 2020 20:06:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.05_model.r WARNING @ Thu, 08 Oct 2020 20:06:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:06:30: #2 You may need to consider one of the other alternative d(s): 1,24,42,525,540,553 WARNING @ Thu, 08 Oct 2020 20:06:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:06:30: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:06:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:06:31: 13000000 INFO @ Thu, 08 Oct 2020 20:06:35: 19000000 INFO @ Thu, 08 Oct 2020 20:06:36: 14000000 INFO @ Thu, 08 Oct 2020 20:06:41: 20000000 INFO @ Thu, 08 Oct 2020 20:06:42: 15000000 INFO @ Thu, 08 Oct 2020 20:06:46: 21000000 INFO @ Thu, 08 Oct 2020 20:06:48: 16000000 INFO @ Thu, 08 Oct 2020 20:06:52: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:06:53: 17000000 INFO @ Thu, 08 Oct 2020 20:06:58: 23000000 INFO @ Thu, 08 Oct 2020 20:06:59: 18000000 INFO @ Thu, 08 Oct 2020 20:07:01: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:07:01: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:07:01: #1 total tags in treatment: 23558680 INFO @ Thu, 08 Oct 2020 20:07:01: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:07:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:07:01: #1 tags after filtering in treatment: 23558680 INFO @ Thu, 08 Oct 2020 20:07:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:07:01: #1 finished! INFO @ Thu, 08 Oct 2020 20:07:01: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:07:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:07:03: #2 number of paired peaks: 148 WARNING @ Thu, 08 Oct 2020 20:07:03: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Thu, 08 Oct 2020 20:07:03: start model_add_line... INFO @ Thu, 08 Oct 2020 20:07:03: start X-correlation... INFO @ Thu, 08 Oct 2020 20:07:03: end of X-cor INFO @ Thu, 08 Oct 2020 20:07:03: #2 finished! INFO @ Thu, 08 Oct 2020 20:07:03: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:07:03: #2 alternative fragment length(s) may be 1,24,42,525,540,553 bps INFO @ Thu, 08 Oct 2020 20:07:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.10_model.r WARNING @ Thu, 08 Oct 2020 20:07:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:07:03: #2 You may need to consider one of the other alternative d(s): 1,24,42,525,540,553 WARNING @ Thu, 08 Oct 2020 20:07:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:07:03: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:07:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:07:04: 19000000 INFO @ Thu, 08 Oct 2020 20:07:07: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:07:10: 20000000 INFO @ Thu, 08 Oct 2020 20:07:15: 21000000 INFO @ Thu, 08 Oct 2020 20:07:20: 22000000 INFO @ Thu, 08 Oct 2020 20:07:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.05_summits.bed INFO @ Thu, 08 Oct 2020 20:07:23: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:07:25: 23000000 INFO @ Thu, 08 Oct 2020 20:07:28: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:07:28: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:07:28: #1 total tags in treatment: 23558680 INFO @ Thu, 08 Oct 2020 20:07:28: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:07:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:07:28: #1 tags after filtering in treatment: 23558680 INFO @ Thu, 08 Oct 2020 20:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:07:28: #1 finished! INFO @ Thu, 08 Oct 2020 20:07:28: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:07:30: #2 number of paired peaks: 148 WARNING @ Thu, 08 Oct 2020 20:07:30: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Thu, 08 Oct 2020 20:07:30: start model_add_line... INFO @ Thu, 08 Oct 2020 20:07:30: start X-correlation... INFO @ Thu, 08 Oct 2020 20:07:30: end of X-cor INFO @ Thu, 08 Oct 2020 20:07:30: #2 finished! INFO @ Thu, 08 Oct 2020 20:07:30: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:07:30: #2 alternative fragment length(s) may be 1,24,42,525,540,553 bps INFO @ Thu, 08 Oct 2020 20:07:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.20_model.r WARNING @ Thu, 08 Oct 2020 20:07:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:07:30: #2 You may need to consider one of the other alternative d(s): 1,24,42,525,540,553 WARNING @ Thu, 08 Oct 2020 20:07:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:07:30: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:07:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:07:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:07:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:07:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:07:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.10_summits.bed INFO @ Thu, 08 Oct 2020 20:07:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:08:06: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:08:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:08:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:08:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120616/SRX9120616.20_summits.bed INFO @ Thu, 08 Oct 2020 20:08:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling